you need to remove water and ions, and also you need a prmtop that matches
(no water or ions)
On 3/1/07, Esther Brugger <esther_brugger.yahoo.com> wrote:
>
> Thanks.
>
> I add igb=1 in the input file, but I get another problem. Since in my
> intial mdcrd files, they have the counter ions and water molecules, now I
> remove the ions and water molecules and get the new mdcrd trajactory file by
> Ptraj in order to get SASA. When I run the Sander, it shows "bad atom type"
> that are corresponding to the counter ions. But If I didn't use prmtop, it
> shows: Unit 8 Error on OPEN: prmtop ( I think prmtop probably should not
> be ignored).
> What I should do now? I really want to solve this problem to get the SASA.
>
> Thanks
>
> *Carlos Simmerling <carlos.simmerling.gmail.com>* wrote:
>
> it won't matter, igb=1 is fine. it only matters if you want to use the GB
> energies.
>
> On 3/1/07, Esther Brugger < esther_brugger.yahoo.com> wrote:
> >
> > Thanks!
> > I remove the water by using ptraj, and doing the calcuation as
> > following:
> >
> > $AMBERHOME/exe/sander -O -i 1_SASA.in -c 1_initial.rst -p 1_wat.prmtop
> > -x 1_SASA.mdcrd -o LV_SASA.out
> >
> > After runing it, it shows:
> > GB/SA calculation is performed only when igb>0
> >
> > I really don't know which option I should select in igb. Could you
> > please give me some suggestions?
> >
> > Thanks a lot!
> >
> > *Carlos Simmerling < carlos.simmerling.gmail.com>* wrote:
> >
> > use ptraj to remove the water with the strip command. you can't
> > calculate SASA with water there.
> > also the -c is not right for the mdcrd file. check the amber manual for
> > details.
> >
> > On 3/1/07, Esther Brugger < esther_brugger.yahoo.com> wrote:
> > >
> > > Thanks for your reply. Here is the command and input file that I used.
> > >
> > > Acturally, this mdcrd trajactory file has the water in it, I want to
> > > remove the water to calculate the SASA, but I really don't know how to do
> > > it. Thanks again for your help!
> > > $AMBERHOME/exe/sander -O -i SASA.in -p prmtop -c mdcrd -o SASA.out
> > > &cntrl
> > > imin = 5,
> > > gbsa=2,
> > > surften=1
> > > /
> > >
> > >
> > >
> > > *Carlos Simmerling < carlos.simmerling.gmail.com>* wrote:
> > >
> > > can you tell us what you did? send the sander run script and input.
> > >
> > > On 2/28/07, Esther Brugger < esther_brugger.yahoo.com > wrote:
> > > >
> > > > Dear Carlos,
> > > >
> > > > Thanks a lot for your reply.
> > > > I tried as you said, it has some prolems when it runs. it shows:
> > > > forrtl: severe (64): input conversion error, unit -5, file Internal
> > > > Formatted Read
> > > > Image PC Routine Line Source
> > > > sander 081A86F6 Unknown Unknown Unknown
> > > > .....
> > > > I don't know why......Do you have any suggestion for that?
> > > > Thanks,
> > > >
> > > >
> > > > *Carlos Simmerling < carlos.simmerling.gmail.com>* wrote:
> > > >
> > > > you might try using the gbsa optino, especially gbsa=2 and
> > > > surften=1. this
> > > > way the SASA energy will actually be the SASA. You can use imin=5 to
> > > > read the
> > > > trajectory and report SASA for each frame.
> > > >
> > > > On 2/28/07, Esther Brugger <esther_brugger.yahoo.com> wrote:
> > > > >
> > > > > Dear Everyone,
> > > > >
> > > > > I am trying to calculate the "solvent accessible surface area
> > > > > (SASA)" of a molecule through a trajectory file obtained by MD simulation
> > > > > (AMBER8). I removed the water molecules (TIP3P model) and counter ions from
> > > > > the systym by using Ptraj. I have some problems to do the calculation of
> > > > > SASA.
> > > > >
> > > > > (1) I checked the archive file for the discussion, it seems
> > > > > "molsurf" program can calculate SASA if I put the proble radius at zero, is
> > > > > it correct? But it need pqrfile, I really don't know how I can get this
> > > > > file. And is it possible to calculate SASA by mdcrd trajectory file in
> > > > > molsurf?
> > > > > (2) Someone suggested to use the software (SURFace) in Honig Lab,
> > > > > but I found it needs the pdb file for the calculations. Is there someone
> > > > > know how to convert the trajactory (mdcrd) file to pdb file for each of the
> > > > > frame?
> > > > > (3) I also found somebody suggested to usd the software
> > > > > "naccess", but I met some problems to decrypt the file, because I
> > > > > didn't find the commands "crypt/des/mcrypt" in my Linux system. Dose someone
> > > > > could give me some suggestions about that?
> > > > >
> > > > > Sorry, I post a lot of questions, I really wish someone could help
> > > > > me to solve these problelms,
> > > > > Thanks for your any help!
> > > > >
> > > > >
> > > > >
> > > >
> > > >
> > > > Esther B.
> > > > ------------------------------
> > > > Bored stiff?<http://us.rd.yahoo.com/evt=49935/*http://games.yahoo.com>Loosen up...
> > > > Download and play hundreds of games for free<http://us.rd.yahoo.com/evt=49935/*http://games.yahoo.com>on Yahoo! Games.
> > >
> > >
> > >
> > >
> > >
> > >
> > > *Carlos Simmerling < carlos.simmerling.gmail.com >* wrote:
> > >
> > > can you tell us what you did? send the sander run script and input.
> > >
> > > On 2/28/07, Esther Brugger <esther_brugger.yahoo.com > wrote:
> > > >
> > > > Dear Carlos,
> > > >
> > > > Thanks a lot for your reply.
> > > > I tried as you said, it has some prolems when it runs. it shows:
> > > > forrtl: severe (64): input conversion error, unit -5, file Internal
> > > > Formatted Read
> > > > Image PC Routine Line Source
> > > > sander 081A86F6 Unknown Unknown Unknown
> > > > .....
> > > > I don't know why......Do you have any suggestion for that?
> > > > Thanks,
> > > >
> > > >
> > > > *Carlos Simmerling < carlos.simmerling.gmail.com> * wrote:
> > > >
> > > > you might try using the gbsa optino, especially gbsa=2 and
> > > > surften=1. this
> > > > way the SASA energy will actually be the SASA. You can use imin=5 to
> > > > read the
> > > > trajectory and report SASA for each frame.
> > > >
> > > > On 2/28/07, Esther Brugger <esther_brugger.yahoo.com> wrote:
> > > > >
> > > > > Dear Everyone,
> > > > >
> > > > > I am trying to calculate the "solvent accessible surface area
> > > > > (SASA)" of a molecule through a trajectory file obtained by MD simulation
> > > > > (AMBER8). I removed the water molecules (TIP3P model) and counter ions from
> > > > > the systym by using Ptraj. I have some problems to do the calculation of
> > > > > SASA.
> > > > >
> > > > > (1) I checked the archive file for the discussion, it seems
> > > > > "molsurf" program can calculate SASA if I put the proble radius at zero, is
> > > > > it correct? But it need pqrfile, I really don't know how I can get this
> > > > > file. And is it possible to calculate SASA by mdcrd trajectory file in
> > > > > molsurf?
> > > > > (2) Someone suggested to use the software (SURFace) in Honig Lab,
> > > > > but I found it needs the pdb file for the calculations. Is there someone
> > > > > know how to convert the trajactory (mdcrd) file to pdb file for each of the
> > > > > frame?
> > > > > (3) I also found somebody suggested to usd the software
> > > > > "naccess", but I met some problems to decrypt the file, because I
> > > > > didn't find the commands "crypt/des/mcrypt" in my Linux system. Dose someone
> > > > > could give me some suggestions about that?
> > > > >
> > > > > Sorry, I post a lot of questions, I really wish someone could help
> > > > > me to solve these problelms,
> > > > > Thanks for your any help!
> > > > >
> > > > >
> > > > >
> > > >
> > > >
> > > > Esther B.
> > > > ------------------------------
> > > > Bored stiff?<http://us.rd.yahoo.com/evt=49935/*http://games.yahoo.com>Loosen up...
> > > > Download and play hundreds of games for free<http://us.rd.yahoo.com/evt=49935/*http://games.yahoo.com>on Yahoo! Games.
> > > >
> > >
> > >
> > >
> > >
> > >
> > > Esther B.
> > > ------------------------------
> > > Finding fabulous fares is fun.
> > > Let Yahoo! FareChase search your favorite travel sites<http://farechase.yahoo.com/promo-generic-14795097;_ylc=X3oDMTFtNW45amVpBF9TAzk3NDA3NTg5BF9zAzI3MTk0ODEEcG9zAzEEc2VjA21haWx0YWdsaW5lBHNsawNxMS0wNw--%0A>to find flight and hotel bargains.
> > >
> >
> >
> >
> >
> >
> > Esther B.
> > ------------------------------
> > Check out the all-new Yahoo! Mail beta<http://us.rd.yahoo.com/evt=43257/*http://advision.webevents.yahoo.com/mailbeta>- Fire up a more powerful email and get things done faster.
> >
>
>
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Received on Sun Mar 04 2007 - 06:07:52 PST
